Head and Neck Cancer

Key Points

HPV Testing in Head and Neck Cancer

Within the head and neck squamous cell cancers (HNSCC), those that are human papilloma virus positive (HPV+) are recognized as a distinct subset based on etiology, molecular-genetic aberrations, and favorable clinical outcomes.  The recent NCCN Clinical Practice Guidelines in Oncology recommend that oropharyngeal SCCs are tested for high risk oncogenic HPV (NCCN guidelines, 2015).   Either immunohistochemistry (IHC) for analysis of p16 expression or in situ hybridization (ISH) for detection of HPV DNA in tumor cell nuclei is recommended.  HPV+ tumors are more common in the tongue and tonsils (lingual and palatine) and tend to occur in younger individuals who do not have the typical risk factors of tobacco smoking and alcohol consumption.

Detection of oncogenic HPV infection in tumors

  • Best method for detection not established; choice depends on specimen available
  • Available options for detecting HPV DNA in tumor cell nuclei


Indications for Testing

  • Persistence of symptoms listed in clinical presentation (see Clinical Background section), particularly hoarseness, sore throat, or dysphagia

Laboratory Testing

  • Refer to Key Points section


  • Gold standard for diagnosis – usually obtained via endoscopy, biopsy, fine needle aspiration of mass
  • Immunohistochemistry and in situ hybridization
    • Refer to Key Points
  • Epstein-Barr virus (EBV) for nasopharyngeal carcinomas

Imaging Studies

  • CT/MRI/PET – establish local and regional extent of disease
    • PET
      • Useful in treatment planning and monitoring
      • Good sensitivity/specificity for detection of nodal metastases


  • Markers
    • HPV – positive tumors have improved prognosis
    • EGFR
      • FISH is sensitive for amplification
      • High levels associated with poor prognosis
      • May be useful in establishing treatment regimens
    • p53 – may predict poor prognosis
    • HER2 – variably expressed but may be associated with improved prognosis
  • Stage at diagnosis helps predict survival
  • Presence of comorbidity – strong predictor of mortality in head and neck cancers
  • Nature and location of tumors
    • Great impact on patient perceptions for future quality of life
    • May determine treatment options that ultimately affect patient mortality

Differential Diagnosis


  • Squamous cell carcinoma (SCC) antigen
    • Monitoring test only – not intended for use in diagnosis
    • Serial determinations (pre- and postsurgery) are necessary – most useful in following cancer recurrence
    • Antigen levels decrease to normal levels ~96 hours after removal of lesion
  • Lipid-associated sialic acid – limited use as a marker in SCC
  • Epstein-Barr virus DNA quantitative PCR – useful for monitoring treatment response and disease progression in nasopharyngeal carcinoma

Clinical Background

Squamous cell carcinoma (SCC) of the head and neck is the most common malignancy (90%) of the upper aerodigestive tract. Less common malignancies include melanoma, sarcoma, lymphoma, and oral metastases.


  • Incidence
    • >55,000 estimated new U.S. cases – represents ~3% of new cancers (NCCN, 2015)
    • >600,000 new cases worldwide
    • Increased incidence over the past 10 years – attributed to increasing prevalence of human papillomavirus (HPV)
      • HPV infection linked to practice of oral sex with multiple sex partners  
      • Cancer of the base of the tongue and tonsils (especially in <45 age group) is the most common etiology of this increased incidence – these cancers are highly related to HPV
  • Age – peaks in 50s
    • Tumors associated with HPV peak in mid 40s
  • Sex – M>F, 3:1
  • Ethnicity – occurs more often in African Americans than Caucasians

Risk Factors

  • Tobacco use – increases risk five- to 25-fold
  • Alcohol abuse – when combined with smoking, risk increases geometrically 
  • Occupational exposures
    • Nickel refining, chromium, mustard gas, radium
    • Woodworking and tanning byproducts
  • Viral infection
    • Epstein-Barr virus – associated with nasopharyngeal carcinoma
    • HPV types 16, 18, 31 – associated with carcinoma of lingual and palatine tonsils
      • Tend not to be associated with smoking or alcohol consumption
  • Betel nut chewing
  • Family history – 1.2- to 2.3-fold higher risk
  • Primary head and neck tumor increases risk for secondary tumors in other head and neck sites and for tumors of lung, esophagus, and other sites sharing similar risk factors


  • Aerodigestive tract is lined with squamous and respiratory epithelium
  • Premalignant disease (epithelial dysplasia) may precede frank malignancy

Clinical Presentation

  • Oral cavity – nonhealing ulcers on the floor of the mouth, tongue, buccal mucosa, and hard palate; persistent sore throat
  • Hypopharynx – hoarseness, dysphagia, otalgia, enlarged cervical nodes
  • Oropharynx – sore throat, otalgia, odynophagia, chronic dysphagia
  • Larynx – hoarseness, shortness of breath; supraglottic (neck mass)
  • Nasopharynx – usually late symptoms of bleeding, obstruction, cranial nerve palsy; otitis media unresponsive to antibiotics  
  • Salivary glands – swelling, adenopathy
  • Paranasal sinuses – obstructions, symptoms occur usually late in disease
  • See Thyroid Cancer for information on thyroid tumors

Indications for Laboratory Testing

  • Tests generally appear in the order most useful for common clinical situations
  • Click on number for test-specific information in the ARUP Laboratory Test Directory
Test Name and Number Recommended Use Limitations Follow Up
Human Papillomavirus (HPV), High Risk by in situ Hybridization, Paraffin 2002899
Method: In situ Hybridization

Preferred in situ hybridization test to detect high-risk HPV subtypes in formalin-fixed, paraffin-embedded tissue

Use to classify equivocal lesions found on biopsy

p16 by Immunohistochemistry 2004064
Method: Immunohistochemistry

Surrogate marker for HPV


HPV ISH testing recommended to confirm HPV

EGFR Gene Amplification by FISH 2008605
Method: Fluorescence in situ Hybridization

Aids in prognostication and therapeutic decisions for neoplasms where amplification has been demonstrated

Tissues fixed in alcohol-based or non-formalin fixatives have not been tested using this method

ERBB2 (HER2/neu) (HercepTest) by Immunohistochemistry, Tissue with Reflex to FISH if 2+ 0049178
Method: Immunohistochemistry

Use as a prognostic marker; may also be useful in established treatment regimen

Reflex pattern – if ERBB2 (HercepTest) result is 2+, then ERBB2 (HER2/neu) Gene Amplification by FISH, Tissue will be added

Epstein-Barr Virus, Quantitative PCR 0051352
Method: Quantitative Polymerase Chain Reaction

Quantify Epstein-Barr virus (EBV) viral load as an aid in monitoring EBV-related disease

Epstein-Barr Virus (EBV) by in situ Hybridization, Paraffin 2002902
Method: In situ Hybridization

Adjunct test for diagnosing nasopharyngeal carcinoma

Additional Tests Available
Click the plus sign to expand the table of additional tests.
Test Name and NumberComments
Lipid Associated Sialic Acid 0080467
Method: Quantitative Spectrophotometry

Limited use as a marker in squamous cell cancer

p53 with Interpretation by Immunohistochemistry 0049250
Method: Immunohistochemistry

Prognostic marker

Squamous Cell Carcinoma Antigen, Serum 0081054
Method: Quantitative Enzyme-Linked Immunosorbent Assay

Limited use as a marker for monitoring